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Magnesium in PDB 1khz: Structure of the Adpr-Ase in Complex with Ampcpr and Mg

Enzymatic activity of Structure of the Adpr-Ase in Complex with Ampcpr and Mg

All present enzymatic activity of Structure of the Adpr-Ase in Complex with Ampcpr and Mg:
3.6.1.13;

Protein crystallography data

The structure of Structure of the Adpr-Ase in Complex with Ampcpr and Mg, PDB code: 1khz was solved by S.B.Gabelli, M.A.Bianchet, M.J.Bessman, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.64 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.100, 67.400, 96.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.7

Other elements in 1khz:

The structure of Structure of the Adpr-Ase in Complex with Ampcpr and Mg also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg (pdb code 1khz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg, PDB code: 1khz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1khz

Go back to Magnesium Binding Sites List in 1khz
Magnesium binding site 1 out of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:19.5
occ:1.00
O B:HOH407 2.0 19.4 1.0
O B:HOH403 2.1 17.4 1.0
OE2 B:GLU116 2.1 19.4 1.0
O1A B:ADV402 2.1 17.6 1.0
OE2 B:GLU164 2.2 22.5 1.0
OE1 B:GLU112 2.2 17.9 1.0
CD B:GLU164 3.1 27.7 1.0
CD B:GLU116 3.2 17.8 1.0
PA B:ADV402 3.2 18.4 1.0
CD B:GLU112 3.2 18.1 1.0
MG B:MG310 3.3 19.5 1.0
OE1 B:GLU164 3.4 26.4 1.0
O2A B:ADV402 3.5 17.3 1.0
MG B:MG304 3.5 23.4 1.0
OE2 B:GLU112 3.6 19.6 1.0
O5' B:ADV402 3.6 19.2 1.0
CG B:GLU116 3.6 16.6 1.0
O B:HOH409 3.6 19.3 1.0
OE1 B:GLU162 3.8 42.1 1.0
O B:ALA96 4.0 18.4 1.0
OE1 B:GLU115 4.2 24.4 1.0
OE1 B:GLU116 4.3 18.4 1.0
C5' B:ADV402 4.4 18.2 1.0
O B:HOH404 4.4 17.1 1.0
CG B:GLU164 4.5 27.7 1.0
CG B:GLU112 4.6 18.7 1.0
CD B:GLU162 4.6 42.7 1.0
CX B:ADV402 4.7 18.9 1.0
OE2 B:GLU162 4.7 45.0 1.0
CA B:GLY97 4.7 15.5 1.0
O B:HOH405 4.7 23.5 1.0
O B:HOH410 4.8 16.1 1.0
CB B:GLU112 4.9 17.4 1.0
O2B B:ADV402 4.9 21.3 1.0
C B:ALA96 5.0 17.2 1.0

Magnesium binding site 2 out of 3 in 1khz

Go back to Magnesium Binding Sites List in 1khz
Magnesium binding site 2 out of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:23.4
occ:1.00
O B:HOH405 1.8 23.5 1.0
O B:HOH407 2.0 19.4 1.0
O B:HOH404 2.2 17.1 1.0
O2A B:ADV402 2.2 17.3 1.0
OE2 B:GLU112 2.2 19.6 1.0
O B:HOH406 2.3 21.6 1.0
CD B:GLU112 3.2 18.1 1.0
PA B:ADV402 3.3 18.4 1.0
OE2 B:GLU162 3.4 45.0 1.0
MG B:MG301 3.5 19.5 1.0
OE1 B:GLU112 3.5 17.9 1.0
O5' B:ADV402 3.6 19.2 1.0
O1A B:ADV402 3.7 17.6 1.0
O B:HOH480 3.8 32.5 1.0
O B:HOH506 4.0 35.6 1.0
NH1 B:ARG111 4.1 24.1 1.0
OE1 B:GLU162 4.1 42.1 1.0
CD B:GLU162 4.1 42.7 1.0
N B:MET98 4.1 20.1 1.0
OE1 B:GLU115 4.2 24.4 1.0
O B:HOH403 4.4 17.4 1.0
CA B:GLY97 4.4 15.5 1.0
O B:MET98 4.6 17.7 1.0
CG B:GLU112 4.6 18.7 1.0
NH2 B:ARG111 4.7 25.0 1.0
CX B:ADV402 4.8 18.9 1.0
C B:GLY97 4.8 17.4 1.0
CZ B:ARG111 4.9 25.4 1.0

Magnesium binding site 3 out of 3 in 1khz

Go back to Magnesium Binding Sites List in 1khz
Magnesium binding site 3 out of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:19.5
occ:1.00
O B:HOH410 2.0 16.1 1.0
O2B B:ADV402 2.1 21.3 1.0
O B:ALA96 2.2 18.4 1.0
OE2 B:GLU116 2.2 19.4 1.0
O B:HOH409 2.3 19.3 1.0
O1A B:ADV402 2.3 17.6 1.0
CD B:GLU116 3.1 17.8 1.0
OE1 B:GLU116 3.2 18.4 1.0
PB B:ADV402 3.3 20.9 1.0
MG B:MG301 3.3 19.5 1.0
PA B:ADV402 3.4 18.4 1.0
C B:ALA96 3.4 17.2 1.0
CX B:ADV402 3.6 18.9 1.0
OE2 B:GLU164 3.7 22.5 1.0
NH2 B:ARG79 3.9 21.9 1.0
O1B B:ADV402 3.9 20.0 1.0
OE1 B:GLU112 4.1 17.9 1.0
O B:HOH425 4.3 21.2 1.0
NE2 B:GLN77 4.3 23.3 1.0
CA B:ALA96 4.3 17.0 1.0
O5' B:ADV402 4.3 19.2 1.0
N B:ALA96 4.3 16.1 1.0
O2A B:ADV402 4.4 17.3 1.0
N B:GLY97 4.4 14.6 1.0
CA B:GLY97 4.5 15.5 1.0
C5' B:ADV402 4.5 18.2 1.0
CG B:GLU116 4.5 16.6 1.0
CB B:ALA96 4.5 16.3 1.0
OR5 B:ADV402 4.6 21.2 1.0
OE1 B:GLN77 4.7 22.2 1.0
CR5 B:ADV402 4.9 22.4 1.0
O B:HOH407 4.9 19.4 1.0
CZ B:ARG79 4.9 20.7 1.0
CD B:GLU164 4.9 27.7 1.0
CD B:GLN77 5.0 20.9 1.0

Reference:

S.B.Gabelli, M.A.Bianchet, Y.Ohnishi, Y.Ichikawa, M.J.Bessman, L.M.Amzel. Mechanism of the Escherichia Coli Adp-Ribose Pyrophosphatase, A Nudix Hydrolase. Biochemistry V. 41 9279 2002.
ISSN: ISSN 0006-2960
PubMed: 12135348
DOI: 10.1021/BI0259296
Page generated: Mon Dec 14 06:20:25 2020

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